Major Histocompatibility Complex Class II Deficiency is a rare primary immunodeficiency disease with autosomal recessive inheritance. It is characterized by the absence of Major Histocompatibility Complex Class II molecules on the surface of immune cells. In this article, we will present a four-month-old baby girl who presented with recurrent fever and progressive exacerbation of respiratory symptoms since a month ago. Relevant examinations suggested pancytopenia, a decrease in CD4 and CD3 ratio, and CD4/CD8 inversion, hypogammaglobulinemia, and diagnosis of hemophagocytic syndrome during treatment which all led to the consideration of the presence of immunodeficiency diseases, and the diagnosis of Major Histocompatibility Complex Class II Deficiency was made by peripheral blood whole-exon sequencing (WES). This case is remarkable in that it reveals features of hemophagocytic syndrome in a Major Histocompatibility Complex Class II Deficiency infant, most probably caused by cytomegalovirus, which rarely reported before, and the Major Histocompatibility Complex Class II Deficiency caused by a novel mutation site in the RFXANK gene which never reported, and it also describes the diagnostic and therapeutic course in detail. In addition, we have summarized the information related to Major Histocompatibility Complex Class II Deficiency triggered by mutations in the RFXANK gene to assist clinicians in early recognition and diagnosis.